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121,962 results • Page 195 of 2440
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Optimizing DNA Sequence Subset Selection for Balanced Base Distribution: Seeking Solutions for Small N Values
optimization evolutionary-algorithm
23 months ago by samuelknudsen ▴ 10
6
votes
8
replies
6.0k
views
7 follow
Which alignment for whole bacterial genomes for phylogenetic tree?
phylogenetic-tree bacterial-genomes
updated 23 months ago by • 0 • written 23 months ago by ▴ 10
1
vote
10
replies
2.8k
views
file conversion from gtf to gff3 for evidence modeler
gff3 stringtie gtf
23 months ago by rj.rezwan ▴ 20
4
votes
0
replies
758
views
Tool: MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders
mybrain-seq miRNA-seq pipeline neuropsychiatry docker
23 months ago by dannyzimm ▴ 50
2
votes
2
replies
1.6k
views
1000 Genomes download files
1000genomes vcf
updated 23 months ago by 45k • written 23 months ago by ▴ 10
1
vote
3
replies
1.4k
views
Porechop demulitplexing of nanopore sequencing data and barcode bins for each sample
porechop
updated 23 months ago by ▴ 600 • written 23 months ago by ▴ 10
0
votes
2
replies
1.2k
views
problem with installing DESEq2
DESeq2
23 months ago by Anvar • 0
0
votes
0
replies
371
views
How to determine the conserved regions in the genome assembly
genome
23 months ago by zhuo • 0
10
votes
17
replies
3.7k
views
Building reference dbSNP file using WGS samples
NGS WGS Variant-calling non-model Bootstrapping
22 months ago by analyst ▴ 70
0
votes
1
reply
781
views
Partition reads in BAM file by MAG
metagenome reads BAM MAG
updated 23 months ago by 20k • written 2.1 years ago by ▴ 10
1
vote
3
replies
1.5k
views
Missing Org.hs.eg.db GO Annotations for Uniprot IDs
Org.hs.eg.db clusterProfiler Uniprot
23 months ago by Charlie ▴ 10
9
votes
7
replies
3.4k
views
6 follow
Can BWA (mem) detect longer deletions?
alignment bwa
updated 23 months ago by 20k • written 2.1 years ago by ▴ 140
1
vote
4
replies
1.3k
views
Detect STRs in illumina library
repeats annotation STR
23 months ago by kirillkirilenko ▴ 40
5
votes
12
replies
4.9k
views
What is the correct procedure to generate a consensus bacterial sequence?
consensus samtools illumina fastq
updated 20 months ago by 20k • written 2.0 years ago by ▴ 760
1
vote
2
replies
1.1k
views
Lower alignment rate when using collapsed reads
short_rna RNA-Seq_mapping collapsed_reads
updated 23 months ago by 20k • written 2.0 years ago by ▴ 40
0
votes
2
replies
1.6k
views
Recommendations for extending contigs from denovo assembly to identify SV insertion sites on chromosome
Nanopore WGS Long-Read SV Assembly
updated 23 months ago by 20k • written 2.0 years ago by ▴ 70
18
votes
41
replies
8.4k
views
6 follow
Convert amino acid sequences into nucleotide sequences
nucleotide protein
updated 22 months ago by 22k • written 2.0 years ago by ▴ 60
1
vote
4
replies
1.5k
views
Viral positive and negative strand with paired sequencing and bowtie
bowtie
23 months ago by Lluís R. ★ 1.2k
0
votes
0
replies
459
views
Functional annotation with nr database followed by GO enrichment analysis
functional-annotation
updated 23 months ago by 45k • written 23 months ago by • 0
1
vote
2
replies
1.2k
views
How to choose the best tool for variant trio analysis
trio WGS GEMINI GATK variant
updated 23 months ago by 20k • written 24 months ago by • 0
2
votes
9
replies
2.2k
views
Aligner with statistics included?
aligner alignment
updated 20 months ago by 20k • written 23 months ago by ▴ 760
3
votes
2
replies
1.5k
views
Estimating Index Hopping
bcl2fastq bclconvert
updated 23 months ago by 20k • written 23 months ago by ▴ 350
0
votes
3
replies
1.0k
views
Discrepancies Between GEO Page and its article - Seeking Clarification
cancer GEO RNA-seq
updated 23 months ago by 45k • written 23 months ago by ▴ 200
4
votes
6
replies
7.1k
views
Conda is installing older version of Spades even though latest version is there in the bioconda repository
python conda spades
updated 23 months ago by 45k • written 2.6 years ago by ▴ 100
4
votes
8
replies
1.8k
views
checkstrand tool (from BBMap suite) question
bbmap checkstrand.sh bbtools
updated 23 months ago by 20k • written 23 months ago by 154k
0
votes
3
replies
898
views
Gene regulatory networks
biological-networks gene-regulatory-networks gene-gene-interaction
updated 23 months ago by 45k • written 23 months ago by • 0
0
votes
0
replies
529
views
using technical replicates for batch bridging of illumina epic methylation data
combat methylation limma epic batch
updated 23 months ago by 45k • written 23 months ago by • 0
1
vote
0
replies
487
views
Help with Enrichr clustergram
enrichr
23 months ago by Chris ▴ 360
1
vote
2
replies
1.2k
views
GWAS in python?
R python GWAS
updated 23 months ago by 45k • written 23 months ago by • 0
2
votes
3
replies
909
views
RNAseq analysis set up - viral infection of bacteria
RNA-seq DESeq2 phage
updated 23 months ago by 154k • written 23 months ago by ▴ 10
1
vote
2
replies
1.4k
views
Help me understand "for stripped" in bcftools isec output
bcftools SNP
updated 23 months ago by 154k • written 23 months ago by ▴ 80
1
vote
4
replies
984
views
Redirecting the output of a command related to another command
unix time
updated 23 months ago by 45k • written 23 months ago by ▴ 10
0
votes
0
replies
480
views
Use of TPM cutoff for Affymetrix GeneChip Genome Arrays
tpm
updated 23 months ago by 103k • written 23 months ago by • 0
3
votes
0
replies
1.0k
views
Herald: The Biostar Herald for Monday, October 16, 2023
herald
23 months ago by Biostar 3.6k
0
votes
0
replies
459
views
Protein protein interactions classification
PPI protein-protein-interaction
updated 23 months ago by 45k • written 23 months ago by ▴ 20
3
votes
8
replies
2.8k
views
Best command line tool for downloading sequencing reads
enaBrowserTools reads Fasterq-dump sequencing
updated 23 months ago by 89k • written 23 months ago by ▴ 30
0
votes
0
replies
1.2k
views
Job: Bioinformatician - R&D and Production Scientist (Liege, Belgium)
genome ngs medicine diagnostics
23 months ago by Leonor Palmeira 3.9k
4
votes
1
reply
1.0k
views
Herald: The Biostar Herald for Monday, October 09, 2023
herald
written 24 months ago by 3.6k
0
votes
1
reply
1.4k
views
map Ensembl gene ID from hg19 to hg38
biomart ensembl
updated 23 months ago by ★ 2.4k • written 24 months ago by ▴ 40
7
votes
7
replies
2.0k
views
Prediction tools summary - zero values
statistics
updated 17 months ago by • 0 • written 24 months ago by ▴ 130
0
votes
0
replies
485
views
ONT methylation data normalization
Methylation Sequencing ONT Statistics Normalization
23 months ago by Rosario • 0
0
votes
0
replies
629
views
News: Course - Flow Cytometry analysis with R/Bioconductor
R Flow-Cytometry Bioconductor
updated 23 months ago by 45k • written 23 months ago by ★ 2.6k
0
votes
0
replies
480
views
KEGG ribosomal gene found in metatranscriptome despite removing rRNA sequences
rRNA KEGG metatranscriptomics
23 months ago by kmat • 0
0
votes
1
reply
820
views
RepBase database for help
RepBase
updated 23 months ago by 45k • written 23 months ago by ▴ 30
2
votes
6
replies
2.5k
views
filter multisample VCF based on Altered AD values
vcf ad filter
updated 23 months ago by ▴ 10 • written 5.4 years ago by ▴ 290
0
votes
2
replies
979
views
DESeq2 Results Annotation
RNA-seq
updated 23 months ago by 45k • written 2.1 years ago by ▴ 30
1
vote
7
replies
2.0k
views
Filtering a 10X generated .bam file based on a list of barcodes
snRNA-seq scRNA-seq samtools BAM RNA-seq
23 months ago by jhnicolas • 0
1
vote
2
replies
1.8k
views
How to properly run prokka on Ubuntu 22?
ubuntu prokka
updated 23 months ago by 45k • written 23 months ago by ▴ 760
0
votes
1
reply
701
views
Removing primers from Amplicon WGBS
Amplicon
updated 23 months ago by 154k • written 23 months ago by • 0
0
votes
2
replies
844
views
Contamination found in sequencing data of an isolated cell structure, what can I do?
DEseq2 RNA-Seq DGE
23 months ago by marina.wakid ▴ 10
121,962 results • Page 195 of 2440
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A: Which is the proper RNA-seq count table transformation to perform hierarchial cl
Answer: Differences between published differential gene expression results and own analy
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
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Answer: Gene expression equivalent of polygenic risk score ? by GouthamAtla 12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
Comment: ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues usin by Ben • 0
write.table(df1, "df1.txt", sep = "\t", row.names = T, col.names = T, quote = FALSE)
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
That is good confirmation. Bacl to the error message. > I don't know how to fix this, given that I already did the trimming steps. DId yo…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
Honestly, those things shouldn't result in a considerable discrepancy. The largest difference will come from the post-processing & analysi…
Answer: Differences between published differential gene expression results and own analy by Ales ▴ 50
I second the comment about comparing the top 100 genes - if you see vastly different results, I would lean closer to examining protocols th…
Answer: Help interpreting BLASTn results and phylogenetic tree for genetics practical by Mensur Dlakic ★ 30k
I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul o…
Answer: Differences between published differential gene expression results and own analy by yura.grabovska ▴ 830
When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
Comment: Functional prediction for proteins of bacteria. by colindaven 8.0k
Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
Comment: Errors with RSEM/bowtie2 by Olivia • 0
Yes, I already made the transcriptome with these tools, and the CD-HIT-EST fasta file is the transcript file that I am using for RSEM. Then…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by Guilherme • 0
Oh, ok. It seems like NCBI stores the files in SRA format (thus needing conversion and database lookups by sra toolkit tools) and EBI store…
Comment: help with modkit on nanopore sequencing data. by andres.firrincieli 3.9k
On the DMR tutorial page, they retrieve Human CpG Islands from the UCSC Table Browser. You can do the same thing for Mouse CpG Islands. Hav…
Comment: After doublet detection in 10x scRNA-Seq data, there is still evidence of double by yura.grabovska ▴ 830
Yes but the problem is that biological knowledge is never fully encompasing. While I can say that a cell expressing CD45 alongside astrocyt…
Comment: DNA copy number blacklist for excluding common unreliable regions by yura.grabovska ▴ 830
Human genome, ideally hg38
Comment: Is Newbler still available for download by anweshaash • 0
Hello, I am wondering if you got access to the software or not. I am looking to use Newbler for my research and I contacted Roche too but t…
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
> I have previously run Trinity with the Trimmomatic step as well as CD-HIT-EST. I assume you did the above to generate the transcriptome,…
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